The AMAPstudio project - Ciradamapstudio.cirad.fr/_media/sg-bresil-oct2011-amapstudio.pdf · Abaqus...

The AMAPstudio project

François de Coligny (INRA-AMAP)Sébastien Griffon (Cirad-AMAP)

1st French-Brazilian FSPM meeting – 26/10/2011

Objectives of AMAPstudio

Objectives :

AMAPstudio is a software suite for plants architecture modelling. It contains applications and models to rebuild, explore, analyse and study the growth of plants from an architectural point of view.

For who :

Scientists and students in the agronomic and botany fields.

2 main softwares :

Applications and models may work at :● the individual plant level in Xplo ● the scene level in Simeo

2 main softwares : Simeo and Xplo

Simeo

Scene Implantation Manager with Edition by Outline is a multi purpose 3D scene editor to (i) create 3D scenes, (ii) export to rendering or other simulation tools, (iii) run scene level 3D evolution models.

2 main softwares : Simeo and Xplo

Xplo

Xplo is a software for plant architecture eXploration at different scales for botanists, agronomists and educational purpose. The main goals are (i) to build, edit, visualize and extract architectural data,(ii) to run individual level 3D growth models.

The AMAPstudio common methodology 1/2

Choose a plant growth model and set initial parameters,

create scenarios by running the model...

... and process interventions (parameters change, pruning, change environment)

2 scenarios

Pruning

The AMAPstudio common methodology 2/2

Use internal tools to check the result

Export data easily to analyse the results in other analysis tools

Opened and documented formats

OPF : Open Plant Format

XML-based format to encapsulate MTG-like representation of the plant architecture ( topology & attributes) + the geometrical data for the 3D reconstruction.

Opened and documented formats

OPS : Open Plant Scene● Documented on : http://amapstudio.cirad.fr/● Mainly used to spatialize OPF files in a scene.● Xplo / Simeo compatible, easy to write, multi-step if necessary.

http://amapstudio.cirad.fr/

Import/export your data in various formats

IMPORT format

Topology :MTG

Geometry :LIG + DTA

Topology + Geometry : OPF (Open Plant Format)

… your formats ...

EXPORT format

Topology :MTG

Geometry :LIG + DTASunflowAbaqusObj (Wavefront)

Topology + Geometry : OPF (Open Plant Format)

… your formats ...

Cecropia MTG Import (P. Heuret) Abaqus export

Software functionnalities overview

Xplo functionalities : plant topology and geometry interactive edition

Interactive topology edition

Xplo functionalities : plant topology and geometry interactive edition

Interactive geometry edition

Xplo functionalities : plant topology and geometry edition by script

Axis geometry model

Needle model 30°

10°

5°

60° (lmax=1.4)

53° (lmax=1)

60° (lmax=1.7)

p

l=p x lmax

Side viewTop view

90°180°

120°

140°

Top view Side view

MTG data import

Illustration : Fir sapling geometrical reconstruction from measurement : O. Taugourdeau

Groovy script

Moresnetia geometrical reconstruction for fossil measurementC.Prestianni, Y. Caraglio

Cecropia geometrical reconstruction. P. Heuret

Xplo functionalities : plant topology and geometry edition by script

Xplo functionalities : data extraction

Topological column Data column

Input source Filter field


Data extraction panel on selected topological column

Extract diameter attribute of the annual shoots (P*)


Extract topological link (e.g. Bearer) of the annual shoots


Extract topological data (e.g. Ramification order) of the annual shoots


Extract topological data (e.g. Position in the axis) of the annual shoots's bearers


Plot data

Extensions : select method to place items in the scene

Extensions : select items to add in the scene

Simplified 3D view of the scene

Rendering parameters

Project manager (scenarios)

Table view of the scene

Rotation, zoom, picking, translation, line/polygon drawing, undo, redo ...

Extensions : export, rendering

Simeo functionalities : scene edition

● Few memory for a lot of individus (database link or files)● Simple 3D visualisation● Import/export ops files ● Interactive edition

e.g. Blender rendering : run Blender renderer from Simeo in background

● Blender : free multi-platform renderer (Windows, Linux, Mac) et pro quality● Others renderer are connected such as Sunflow.

Simeo functionalities : scene rendering

GL-PNN : Black pines simulated with PNN (Capsis module) and Greenlab. Rendered with Sunflow.

Lu FENG, Philippe DE REFFYE, Philippe DREYFUS, Daniel AUCLAIR

Simeo : scene rendering

Simeo functionalities : scene irradiance

Archimed connection

AMAPstudio functionalities : Xplo and Simeo are linked

Axis geometry model

Needle model

Individual scale Scene scale

Scene reconstruction

Radiative model

30°

10°

5°

60° (lmax=1.4)

53° (lmax=1)

60° (lmax=1.7)

p

l=p x lmax

Side viewTop view

90°180°

120°

140°

Top view Side view

Objectives: Evaluate effect of light environment on fir sapling architecture O. Taugourdeau

How to integrate/run a plant growth simulator ?

Simeo software architecture

Xplo software architecture

AMAPstudio SDK

AMAPstudio : ● Libraries :

● Maths : common math functions● Formats : OPF, OPS, MTG readers/writers● Sketch : MVC GUI library● Structures : ArchiTree and Geometry builder.● SimulationTools : Scheduler, Listeners, Meristems,

Organs.● Utils : common usefull functions (e.g. AutoUI)

● Workspace : ● Sunflower model● Principes model● Draft model● Greenlab model● ...

● Xplo :● Kernel● Gui● Extensions● Modules :

● PlantEditor● Sunflower ● Greenlab● ..

● Simeo :● Kernel● Gui● Extensions● Modules :

● AmapScene● Greenlab

Modeller inputs

Greenlab FSPM : Feng Lu, Ph. de Reffye, S. Griffon.

Common Pool

B

PF

M

I

Automaton

Architecture,Allometry,Geometry

leaves

roots

Automaton

fruitsphotosynthesis

H2O

Pool of biomass

transpiration

CHO

seedbranches

GC i, Qi-1

i ++, QiOrgan mass, leaves surface

Organ nb, Organ demand

GCi

ArchiTree

Function

Partition

Simulators developped with AMAPstudio SDK

Greenlab FSPM : Feng Lu, Ph. de Reffye, S. Griffon.

Fitting


Illustration : Sunflower : growth and development model : H. Rey.

0.0.E+00

5.0.E+05

1.0.E+06

1.5.E+06

2.0.E+06

2.5.E+06

0 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400

S1_1

I1_1

S2_1

C1_1

C1_31

C1_32

I2_1

C2_1C2_1H

0%

20%

40%

60%

80%

100%

0 200 400 600 800 1000 1200 1400

Organ size is computed from logistics and radiative balance.

Development and growth are relative to sum of degrees day.


Illustration : Palm tree: Palm tree architecture growth model.H. Rey, R. Lecoustre.

Multiscale structure of palm tree Excel parameter file


Root types

Each type has its own behaviour: - Apical growth- Branching- Death, pruning.

Parameters are indexed according positions on the root.

Illustration : DigR: root structural growth model .JF. Barczi , H. Rey and Christophe Jourdan


Digiplante

Seed plants and trees according to various patterns.Compute Delaunay triangulation and the linked Voronoi diagram.Export to Digiplante for simulation (each plant get his own area).Rendering.

External simulators linked to AMAPstudio

A Forest Growth Simulator Based on Functional-Structural Modelling of Individual Trees, 2009. Paul-Henry Cournède, Thomas Guyard, Benoit Bayol, Sébastien Griffon, François de Coligny, Philippe Borianne, Marc Jaeger, Philippe de Reffye. Third International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications (PMA09), Beijing : Chine (2009)

Digiplante



CalRGB software :

M. Jaeger

SLE software : S. Griffon

Video

Script mode for repetitive simulations

DevelopersModellersEnd-users

D M U

The AMAPstudio Community:

Developers + Modellers are co-developping together

Actors roles:

Developers: computer developers, design, training courses, assistance

Modellers: scientists, build their models inside AMAPstudio

End-users: interested by using the models

The AMAPstudio project organisation

The AMAPstudio charter:

1. Free kernel: the AMAPstudio kernel is a free software (LGPL licence)

2. Development: the modelers are in charge of the development of their models

3. Support: They can have support from the developers

4. Free access in the community: All the source codes are freely accessible by all members in the AMAPstudio community

5. Respect of intellectual property: all members respect the intellectual property of the other members

6. Validations: developers deal with technical validation, modelers deal with functionnal validation

7. Distribution: the stabilized / validated modules may be distributed when the author decides and chooses a licence

8. Decentralization: modelers manage directly the relations with their end-users

mo

du

le 1

gui

scr

mo

du

le 2

gui

mo

du

le 3

gui

scri

pt

pilo

t

gu

i pilo

t

kernel

Library 1

library 2

library 1ext 2

ext 3

ext 1Clear participation rules

The AMAPstudio charter

The AMAPstudio website

http://amapstudio.cirad.fr

● News● Documention● Projects● Download (web demo version)● FAQ● SVN access registration● ...

AMAPstudio technical informations

● Developped in Java (multi-platform), under LGPL licence.● 3D OpenGL ● Versioning system : SVN

The AMAPstudio project - Ciradamapstudio.cirad.fr/_media/sg-bresil-oct2011-amapstudio.pdf · Abaqus...

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